My system is an Ubuntu 9.10 32bit:
#uname -a
Linux cavemanpc 2.6.31-22-generic #63-Ubuntu SMP Wed Aug 18 22:54:26 UTC
2010 i686 GNU/Linux

# free -m
             total       used       free     shared    buffers     cached
Mem:          3000       1847       1152          0        120        961
-/+ buffers/cache:        766       2234
Swap:         4769          0       4769

My Ubuntu XML related packages:
root@cavemanpc:~# dpkg -l | grep -i libxml | awk '{ print $2}'
libxml++2.6-2
libxml++2.6-dev
libxml-commons-external-java
libxml-commons-resolver1.1-java
libxml-java-openoffice.org
libxml-parser-perl
libxml-twig-perl
libxml-xpath-perl
libxml2
libxml2-dev
libxml2-utils
libxmlgraphics-commons-java
python-libxml2

Thanks

Caveman



On Wed, Aug 25, 2010 at 12:43 AM, Orvalho Augusto <orvaquim@gmail.com>wrote:

> It seems to be a bug on the XML package.
>
> This is what I run (and it is not the only file):
> > library("XML")
> > doc <- xmlDoc("Malaria_Grave.xml")
>
>  *** caught segfault ***
> address 0x9, cause 'memory not mapped'
>
> Traceback:
>  1: .Call("RS_XML_createDocFromNode", node, PACKAGE = "XML")
>  2: xmlDoc("Malaria_Grave.xml")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection: 1
> aborting ...
> Segmentation fault
>
> ##=========================
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> i686-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] XML_3.1-1
> >
>
> ##=========================
>
> Thanks
> Caveman
>
>
> On Wed, Aug 25, 2010 at 12:02 AM, Gavin Simpson <gavin.simpson@ucl.ac.uk>wrote:
>
>> On Tue, 2010-08-24 at 23:35 +0200, Orvalho Augusto wrote:
>> > I have one XML file with 30MB that I need to read the data.
>> >
>> > I try this;
>> > library(XML)
>> > doc <- xmlDoc("Malaria_Grave.xml")
>> >
>> > And R answers like this
>> >  *** caught segfault ***
>> > address 0x5, cause 'memory not mapped'
>>
>> This is most likely a bug in your version (unstated) of the XML package.
>> But it may be a problem with the file, though XML shouldn't crash R.
>> Make sure you are using the latest version of the XML package and R is
>> up-to-date, then retry your code in a new R session. If it still
>> segfaults, you need to file a bug report with the maintainer: Duncan
>> Temple Lang, and include all the relevant details such as output from
>>
>> sessionInfo()
>>
>> The .xml file you are trying to read and the code required to reproduce
>> the segfault.
>>
>> HTH
>>
>> G
>>
>> > Traceback:
>> >  1: .Call("RS_XML_createDocFromNode", node, PACKAGE = "XML")
>> >  2: xmlDoc("Malaria_Grave.xml")
>> >
>> > Possible actions:
>> > 1: abort (with core dump, if enabled)
>> > 2: normal R exit
>> > 3: exit R without saving workspace
>> > 4: exit R saving workspace
>> >
>> >
>> > Or I try this:
>> > doc <- xmlTreeParse("Malaria_Grave.xml")
>> >
>> > I get this
>> > xmlParseEntityRef: no name
>> > xmlParseEntityRef: no name
>> > Error: 1: xmlParseEntityRef: no name
>> > 2: xmlParseEntityRef: no name
>> >
>> > Please guys help this simple mortal!
>> > Caveman
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
>>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
>> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>>
>>
>
>
>
>

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